Compositions of microbiota and methods related thereto

Abstract

Methods and compositions are provided for treating weight related conditions and metabolic disorders by altering microbiota in a subject. One aspect provides methods and compositions to alter microbiota in a subject by administering to the subject a composition that includes a substantially purified microbiota from phyla such as Bacteroidetes, Proteobacteria, Firmicutes and Verrucomicrobia or orders such as Bacteroidales, Verrucomicrobiales, Clostridiales and Enterobacteriales or genera such as Alistipes, Clostridium, Escherichia , and Akkermansia . Another aspect includes a pharmaceutical composition for altering microbiota that includes a therapeutically effective amount of substantially purified microbiota and a pharmaceutically acceptable carrier. Yet another aspect includes methods for treating a disorder, such as obesity, in a subject in need of such treatment by changing relative abundance of microbiota in a gastrointestinal tract of the subject without or in addition to a surgical procedure.

What is claimed is: 
     
       1. A pharmaceutical composition for altering microbiota comprising:
 a therapeutically effective amount of a substantially purified  Akkermansia , wherein the substantially purified  Akkermansia  comprises at least 50% of a strain of  Akkermansia,    
 a prebiotic, and 
 a pharmaceutically acceptable carrier, wherein the pharmaceutical composition is formulated for oral delivery and encapsulated by a coating, wherein the coating does not fully degrade until after it exits the stomach of a subject. 
 
     
     
       2. The pharmaceutical composition of  claim 1 , further comprising at least one of a substantially purified Bacteroidetes, a substantially purified Firmicutes and a substantially purified Proteobacteria. 
     
     
       3. The pharmaceutical composition of  claim 2 , wherein the substantially purified Bacteroidetes is Bacteroidales, the substantially purified Firmicutes is Clostridiales and the substantially purified Proteobacteria is Enterobacteriales. 
     
     
       4. The pharmaceutical composition of  claim 2 , wherein the substantially purified Bacteroidetes is  Alistipes , the substantially purified Firmicutes is  Clostridium  and the substantially purified Proteobacteria is  Escherichia.    
     
     
       5. The pharmaceutical composition of  claim 1 , wherein the pharmaceutical composition alters the relative abundance of at least one of Bacteroidetes, Verrucomicrobia, Firmicutes, Tenericutes, and Proteobacteria in a gastrointestinal tract of a subject. 
     
     
       6. The pharmaceutical composition of  claim 1 , wherein the prebiotic is a non-digestible oligosaccharide. 
     
     
       7. The pharmaceutical composition of  claim 6 , wherein the non-digestible oligosaccharide is a fructooligosaccharide, a glucooligosaccharide, a xylooligosaccharide, a galactooligosaccharide, an arabinoxylan, an arabinogalactan, a galactomannan, a polydextrose, an oligofructose, inulin, and/or a derivative thereof. 
     
     
       8. The pharmaceutical composition of  claim 6 , wherein the non-digestible oligosaccharide is a fructooligosaccharide. 
     
     
       9. The pharmaceutical composition of  claim 1 , wherein the prebiotic is inulin. 
     
     
       10. The pharmaceutical composition of  claim 1 , wherein the pharmaceutical composition is formulated for delivery to a small intestine, a large intestine, an ileum, a cecum, or a colon region of a subject. 
     
     
       11. The pharmaceutical composition of  claim 10 , wherein the pharmaceutical composition is formulated for delivery to an ileum or a colon region of a subject. 
     
     
       12. The pharmaceutical composition of  claim 1 , further comprising substantially purified Firmicutes. 
     
     
       13. The pharmaceutical composition of  claim 12 , wherein the substantially purified Firmicutes is substantially purified Clostridiales. 
     
     
       14. The pharmaceutical composition of  claim 13 , wherein the pharmaceutical composition comprises between about 30% and about 60% substantially purified Clostridiales. 
     
     
       15. The pharmaceutical composition of  claim 12 , wherein the substantially purified Firmicutes is substantially purified  Clostridium.    
     
     
       16. The pharmaceutical composition of  claim 15 , wherein the pharmaceutical composition comprises between about 30% and about 50% substantially purified  Clostridium.    
     
     
       17. The pharmaceutical composition of  claim 1 , wherein the pharmaceutical composition increases a relative abundance of  Clostridium  in a subject. 
     
     
       18. The pharmaceutical composition of  claim 1 , wherein the pharmaceutical composition increases glucose metabolism in a subject. 
     
     
       19. The pharmaceutical composition of  claim 1 , wherein the pharmaceutical composition increases energy expenditure in a subject. 
     
     
       20. The pharmaceutical composition of  claim 1 , wherein the  Akkermansia  is lyophilized. 
     
     
       21. The pharmaceutical composition of  claim 1 , wherein if the composition comprises a mixture of bacterial strains, then at least 50% of the bacterial strains in the composition are Verrucomicrobia, Bacteroidetes, Firmicutes, or Proteobacteria. 
     
     
       22. The pharmaceutical composition of  claim 1 , wherein the  Akkermansia  is viable. 
     
     
       23. The pharmaceutical composition of  claim 1 , wherein the pharmaceutical composition comprises two or more bacterial strains, wherein the two or more bacterial strains exhibit a synergistic effect in the pharmaceutical composition.